Senior Scientist

Research Statement

I am an ecosystems ecologist with roots in mechanistic plant physiology. For two decades, I have striven to understand controls over dynamic interactions among plants, microbes, and soils, particularly in the fundamental terrestrial commodities exchange -- the rhizosphere. In the rhizosphere, organic carbon (from plants) fuels recycling of mineral nutrients (by microbes), maintaining the productivity on which ecosystems and humanity depend. My work combines organismal, hydrologic, soil physical, and ecosystems perspectives and aims to identify commonalities across systems in how organism-initiated flow (of water) and physical (soil) structure constrain, and promote, resource exchange. Such commonalities should extend to any system where interacting macro- and microorganisms (microbiomes) are embedded in, evolving in, and creating or shaping their complex physical environment. I also have particular interest in desiccation tolerance and photoprotective mechanisms among desert-dwelling, unicellular green algae, as a window into adaptations enabling the leap of diverse green plants from aquatic habitats to land. My work is interdisciplinary and collaborative, combining development of genetically engineered microbiosensors, chlorophyll fluorescence and gas exchange, in situ imaging,”omics” approaches and new stable isotope techniques, with organismal- and ecosystems-scale modeling.

Current Projects

“Does Chloroplast Thylakoid Membrane Organization Influence Desiccation Tolerance in Green Algae?”
DOE Environmental Molecular Sciences Laboratory (EMSL) Science Theme Project 48938
PI: Zoe Cardon, Ecosystems Center, MBL
EMSL collaborator: Galya Orr, EMSL and PNNL.
We are studying photoprotection during desiccation in multiple, evolutionarily independent terrestrial green algal lineages found in desert microbiotic crusts of the Southwestern U.S. We will work with EMSL personnel to examine whether thylakoids stack into grana in chloroplasts of a diverse range of green algae, all isolated from desert microbiotic crusts, but demonstrated in our assays to have a repeatable difference in their ability to recover photosynthesis during rehydration after desiccation. Structured illumination microscopy, TEM, and confocal fluorescence imaging will all be applied to a suite of ten diverse desert green algal taxa to discern whether thylakoids are stacked in grana, and whether the presence/absence/extent of stacking correlates with the strength of observed desiccation-induced photoprotection.

“3D Reality Check: Developing Structural Support for Predicting Microbial Function andInterpreting Microbial ‘Omics’ Data”
DOE Joint Genome Institute – Environmental Molecular Sciences Laboratory (JGI-EMSL) Collaborative Science 48984, 49028
Lead PI: Zoe Cardon, Ecosystems Center, MBL
Co-Is: Joe Vallino and Gretta Serres, MBL
EMSL collaborator: Tim Scheibe, EMSL and PNNL.
To understand how environmental microheterogeneity and 3D soil structure affect microbial activities and biogeochemical function at the scales microbes experience, a modeling framework is needed that operates at spatial scales relevant to microbes, that can incorporate 3D structural information from real soils, and that includes diffusion and advection of resources and biological signals, geochemical reactions, and microbial activities. This project contributes to development and testing of such a pore-scale computational framework. The project focuses on a physically simple test case exploring how diffusion and advection of the solute acetate and the gases H2 and CO2 affect measured and modeled gene expression associated with production of methane by the JGI-sequenced methanogen Methanosarcina barkeri str. Fusaro. The work is designed to be a “proof of concept” using M. barkeri cultured in microcosms with known 3D pore-scale physical structure created by very accurately sized sand. Transcriptomes (sequenced by JGI) will be gathered from M. barkeri cultured in microcosms hosting acetoclastic, hydrogeneotrophic, or mixed metabolisms. These gene expression data will be compared with methanogenesis pathway induction predicted for millions of microcosm locations modeled by the pore-scale computational framework, in which a genome-scale, flux-balance based model of M. barkeri metabolism will be embedded.

“Collaborative Research: MSB: The Role of Sulfur Oxidizing Bacteria in Salt Marsh C and N Cycling”
NSF Division of Environmental Biology DEB-1050713
PIs (MBL): Zoe Cardon and Anne Giblin, Ecosystems Center, MBL
PI (WHOI): Stefan Sievert, Biology
Salt marshes are extraordinarily productive ecosystems found in estuaries worldwide, but many receive high nitrate input from land, degrading water quality, and leading to harmful algal blooms and low oxygen zones harmful to fish. We are investigating environmental and microbial controls over the fate of nitrate in salt marshes, in lab and field experiments at Plum Island Ecosystems LTER and the MBL Research Greenhouse. We are focusing on sulfur-oxidizing bacteria -- chemosynthetic microbes that use energy trapped in sulfur compounds in sediment to grow. Many of these bacteria can use nitrate as a terminal electron acceptor, transforming it either into dinitrogen gas (N2) via denitrification, or ammonium (NH4+) via DNRA, thus affecting the fate of pollutant nitrate in the marsh. We are (1)identifying sulfur-oxidizers present in sediment densely populated with the salt marsh grass, Spartina alterniflora, and examining their gene expression linked to sulfur and nitrate processing under shifting environmental conditions; and (2) combining this molecular information with measurements of rates and characteristics of biogeochemical reactions occurring in the sediment.

“Hydraulic redistribution of water through plant roots – implications for carbon cycling and energy flux at multiple scales”
DOE Terrestrial Ecosystems Science DE-SC0008182
PI: Zoe Cardon, Ecosystems Center, Ecosystems Center, MBL
Co-PIs: Rebecca Neumann, University of Washington; Guiling Wang & Daniel Gage, University of Connecticut
This project aims to advance quantitative and predictive understanding of “hydraulic redistribution” (HR) in seasonally dry ecosystems. During HR, soil water moves upward, downward, or horizontally from moist to dry soil through plant roots, which serve as conduits connecting soil volumes. Using a linked suite of empirical experiments, small-scale mechanistic modeling (using the reactive transport model Min3P), and terrestrial ecosystem and earth system modeling (using CLM4.5 modified with a version of Ryel et al.’s 2002 HR model), we are exploring HR’s impact on terrestrial carbon, nitrogen, water, and energy cycles. Large scale modeling draws from greenhouse and field data (from 8 Ameriflux sites), and incorporates information from mechanistic modeling in order to improve the representation of HR in earth system models and to quantify the effects of HR on terrestrial ecosystems in past and future regional climates.

“Photoprotection in Diverse, Desiccation-Tolerant, Desert Green Algae and Their Close Aquatic Relatives”
NSF Integrative Organismal Systems IOS-1355085
Lead PI: Zoe Cardon, Ecosystems Center, MBL
Collaborator: Doug Bruce, Brock University, Ontario, Canada
A key step in the evolution of diverse life on Earth was the expansion of organisms’ territories from living in water to surviving on land. Green plants are by far the largest group of advanced photosynthetic organisms to have become established and diversified on land. Flowering plants, evergreen conifers, mosses, and ferns have long been studied for clues to the traits important for terrestrial survival, however, they are all descended from a single green algal ancestor that successfully invaded land. Traits they share may be essential for surviving the rigors of terrestrial life, or they might simply be traits inherited from the common ancestor, as evolutionary baggage. To tease apart these two possibilities, other green, photosynthetic, terrestrial organisms must be studied that are not descended from that common green algal ancestor. Such a suite of organisms is found among diverse, free-living, microscopic green algae inhabiting microbiotic crusts of the desert Southwestern U.S. The objective of this research is to determine the process(es) underlying a very powerful mechanism protecting the photosynthetic apparatus of green algae isolated from microbiotic crusts, during desiccation and rehydration.Understanding desiccation tolerance mechanisms is important because these desert green algae share many characteristics with larger agriculturally and ecologically important green plants, and also with the green algae increasingly used for biofuel production.

"Integration of Pore-Scale Simulations and Multi-Omics Data to Develop Insights into Functional Heterogeneity in Microbial Communities"
DOE Environmental Molecular Sciences Laboratory (EMSL) Science Theme Project 48391
Lead PI: Zoe Cardon, Ecosystems Center, MBL
Co-Is: Joe Vallino and Gretta Serres, MBL
EMSL collaborator: Tim Scheibe, EMSL and PNNL.
This project aims to develop a computational framework, on the CASCADE supercomputer at PNNL, that embeds very diverse microbial community structure and function within high resolution 3D environmental structure at pore (tens of micrometer) scales. The work emerges from fundamental questions in basic and applied microbial ecology:
• How does 3D microenvironmental structure affect, and how is it affected by, microbial community structural diversity and expression of microbial function?
• How does environmental microheterogeneity affect resulting process rates measured at larger scales, and our ability to predict them, e.g. in bioremediation, ecosystem function, food, or fuel production?
This approach recognizes biotic information in “omics” datasets as a signal resulting from structured interaction between the microbiotic and the abiotic at microscales. Recognizing this interaction will support greater understanding of how microbial functional and community diversity in natural and man-made ecosystems persist.

“A novel low-waste, low-maintenance system for microbial generation of methane from algal biomass”
Anonymous donor
PIs: Zoe Cardon and Joe Vallino, Ecosystems Center, MBL
Using a suite of algal species, and a variety of mixed decomposer and methanogenic microbial communities, this project aims to maximize methane production from algal biomass, with minimal maintenance requirements and waste production by the system.